Mercurial > repos > lecorguille > xcms_report

--- a/report.html	Wed Dec 23 09:30:33 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<!DOCTYPE html>
-<HTML lang='en'>
-<HEAD>
-<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
-<title>[W4M] XCMS analysis report</title>
-<style>
-table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}
-th { background: #898989; text-align:left;}
-tr { border: 1px solid #000000 }
-h2 { color: #FFA212; }
-ul li { margin-bottom:10px; }
-</style>
-</HEAD>
-<BODY>
-<h1>___ XCMS analysis report using Workflow4Metabolomics ___</h1>
-<h2>Samples used:</h2>
-<table
-<tr><th>sample</th><th>filename</th></tr>
-<tr><td> HU_neg_051 </td><td> sacuri//bio2/HU_neg_051.mzXML </td></tr><tr><td> HU_neg_060 </td><td> sacuri//bio2/HU_neg_060.mzXML </td></tr><tr><td> HU_neg_017 </td><td> sacuri//bio/HU_neg_017.mzXML </td></tr><tr><td> HU_neg_028 </td><td> sacuri//bio/HU_neg_028.mzXML </td></tr><tr><td> Blanc04 </td><td> sacuri//blank/Blanc04.mzXML </td></tr><tr><td> Blanc06 </td><td> sacuri//blank/Blanc06.mzXML </td></tr>
-</table>
-<h2>Function launched:</h2>
-<table>
-<tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>
-<tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
-<td>nSlaves</td><td>1</td></tr>
-<tr><td>method</td><td>matchedFilter</td></tr>
-<tr><td>step</td><td>0.01</td></tr>
-<tr><td>fwhm</td><td>30</td></tr>
-<tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td>
-<td>method</td><td>density</td></tr>
-<tr><td>sleep</td><td>0.001</td></tr>
-<tr><td>minfrac</td><td>0.5</td></tr>
-<tr><td>bw</td><td>30</td></tr>
-<tr><td>mzwid</td><td>0.25</td></tr>
-<tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
-<td>method</td><td>chrom</td></tr>
-</table>
-<h2>Information about the xcmsSet object:</h2>
-<pre>
-An "xcmsSet" object with 6 samples
-
-Time range: 16.3-1138.9 seconds (0.3-19 minutes)
-Mass range: 61.9883-481.2446 m/z
-Peaks: 1799 (about 300 per sample)
-Peak Groups: 289
-Sample classes: bio, bio2, blank
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 0.421 MB
-</pre>
-<h2>Citations:</h2>
-<ul>
-<li>To cite the <b>XCMS</b> package in publications use:
-<ul>
-<li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
-<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
-<li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
-</ul>
-</li>
-<li>To cite the <b>CAMERA</b> package in publications use:
-<ul>
-<li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
-</ul>
-</li>
-<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
-<ul>
-<li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics  doi:10.1093/bioinformatics/btu813</li>
-</ul>
-</li>
-</ul>
-</BODY>
-</HTML>
--- a/repository_dependencies.xml	Wed Dec 23 09:30:33 2015 -0500
+++ b/repository_dependencies.xml	Wed Dec 23 09:30:44 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-	<repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	<repository name="rdata_xcms_datatypes" owner="lecorguille" />
 </repositories>